From ac1a397024f55dc6f7753f72dc579017165a2026 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Mon, 29 Sep 2014 11:40:10 -0400
Subject: [PATCH] This warning message actually happens all the time in
 AssessNA12878 when we subset down to biallelic events but I've verified that
 it is working as intended. Moving the logging level up to debug.

---
 .../gatk/utils/variant/GATKVariantContextUtils.java             | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
index f818d8d33..a099d8c9c 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java
@@ -706,7 +706,7 @@ public class GATKVariantContextUtils {
                 if ( likelihoodIndexesToUse == null ) {
                     newLikelihoods = originalLikelihoods;
                 } else if ( originalLikelihoods.length != expectedNumLikelihoods ) {
-                    logger.warn("Wrong number of likelihoods in sample " + g.getSampleName() + " at " + vc + " got " + g.getLikelihoodsString() + " but expected " + expectedNumLikelihoods);
+                    logger.debug("Wrong number of likelihoods in sample " + g.getSampleName() + " at " + vc + " got " + g.getLikelihoodsString() + " but expected " + expectedNumLikelihoods);
                     newLikelihoods = null;
                 } else {
                     newLikelihoods = new double[likelihoodIndexesToUse.size()];